Merge remote-tracking branch 'origin/main' into kaushik-oct-2018

and apply suggestions from @tobyhodges

Author: mr-c

.github/workflows/documentation-links.yaml

@@ -0,0 +1,20 @@
+# https://github.com/readthedocs/actions/tree/v1/preview#how-to-use-it
+name: Read the Docs Pull Request Preview
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "common-workflow-languageuser-guide"
+          project-language: "en"
+          # message-template: ?
+          platform: "community"

.github/workflows/gh-pages.yaml

@@ -0,0 +1,56 @@
+name: GitHub Pages sphinx deployment
+
+on:
+  push:
+    branches:
+      - release
+  workflow_dispatch:
+
+# NOTE: If you modify this file to install a package with pip or apt, please
+#       verify if we need the same package added to our readthedocs build.
+jobs:
+  # Ref: https://stackoverflow.com/questions/57989790/using-github-actions-to-publish-documentation
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install apt packages
+        run: |
+          sudo apt-get install -y graphviz tree
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+
+      - name: Upgrade pip
+        run: |
+          # pip >= 20.1 so we can use ``pip cache dir``
+          python3 -m pip install --upgrade pip
+      - name: Get pip cache dir
+        id: pip-cache
+        run: echo "::set-output name=dir::$(pip cache dir)"
+
+      - name: Cache dependencies
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.pip-cache.outputs.dir }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install dependencies
+        run: python3 -m pip install -U -e .[all]
+
+      - name: pre-pull container images
+        run: make container-pull
+
+      - name: Build documentation
+        run: make html
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build/html/
+          publish_branch: gh-pages

.gitignore

@@ -3,9 +3,15 @@
 .DS_Store
 .ipynb_checkpoints
 .sass-cache
+.jekyll-cache/
 __pycache__
 _site
 .Rproj.user
 .Rhistory
 .RData
+_build/
+build/
+*.egg-info/
 
+src/_includes/cwl/**/output.txt
+venv/

.readthedocs.yaml

@@ -0,0 +1,23 @@
+version: 2
+
+# NOTE: If you modify this file to install a package with pip or apt, please
+#       verify if we need the same package added to our CI.
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+    nodejs: "16"
+  apt_packages:
+    - graphviz
+    - tree
+
+sphinx:
+  configuration: src/conf.py
+  builder: html
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - all

.travis.yml

@@ -1,19 +1,21 @@
-sudo: required
 services:
   - docker
 
 language: python
 python:
-  - 2.7
-  - 3.6
+  - 3.8
+
+cache:
+  pip: true
 
 branches:
   only:
-    - gh-pages
+    - main
     - /.*/
 
-before_script:
-  - pip install cwltool cwltest html5lib
+install:
+  - pip install -U pip setuptools wheel typing
+  - pip install -e .[all]
 
 script:
   - make RUNNER=cwltool unittest-examples

AUTHORS renamed to AUTHORS.md

@@ -0,0 +1,61 @@
+# Citation
+
+To cite the Common Workflow Language project in a scholary work, please use:
+
+Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić,
+Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, and The CWL Community. 2022.
+Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.
+Commun. ACM 65, 6 (June 2022), 54–63. https://doi.org/10.1145/3486897
+
+```
+@article{10.1145/3486897,
+author = {Crusoe, Michael R. and Abeln, Sanne and Iosup, Alexandru and Amstutz, Peter and Chilton, John and Tijani\'{c}, Neboj\v{s}a and M\'{e}nager, Herv\'{e} and Soiland-Reyes, Stian and Gavrilovi\'{c}, Bogdan and Goble, Carole and Community, The CWL},
+title = {Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language},
+year = {2022},
+issue_date = {June 2022},
+publisher = {Association for Computing Machinery},
+address = {New York, NY, USA},
+volume = {65},
+number = {6},
+issn = {0001-0782},
+url = {https://doi.org/10.1145/3486897},
+doi = {10.1145/3486897},
+abstract = {Standardizing computational reuse and portability with the Common Workflow Language.},
+journal = {Commun. ACM},
+month = {may},
+pages = {54–63},
+numpages = {10}
+}
+```
+
+To cite just the CWL standards themselves, please use the following inclusive of the DOI:
+
+Amstutz, Peter; Crusoe, Michael R; Tijanić, Nebojša; Chapman, Brad;
+Chilton, John; Heuer, Michael; Kartashov, Andrey; Kern, John; Leehr, Dan;
+Ménager, Hervé; Nedeljkovich, Maya; Scales, Matt; Soiland-Reyes, Stian;
+Stojanovic, Luka (2016): Common Workflow Language, v1.0. Specification,
+Common Workflow Language working group. https://w3id.org/cwl/v1.0/
+https://dx.doi.org/10.6084/m9.figshare.3115156.v2
+
+```
+@data{cwl,
+  doi = {10.6084/m9.figshare.3115156.v2},
+  url = {https://doi.org/10.6084/m9.figshare.3115156.v2},
+  author = {Peter Amstutz; Michael R. Crusoe; Nebojša Tijanić; Brad Chapman;
+John Chilton; Michael Heuer; Andrey Kartashov; John Kern; Dan Leehr;
+Hervé Ménager; Maya Nedeljkovich; Matt Scales; Stian Soiland-Reyes;
+Luka Stojanovic
+ },
+  publisher = {Figshare},
+  institution = {Common Workflow Language working group},
+  title = {Common Workflow Language, v1.0},
+  year = {2016}
+}
+```
+
+[//]: # (the above is from https://github.com/common-workflow-language/common-workflow-language/blob/main/CITATION.cff)
+
+Our preferred DOI for the "CWL User Guide" is http://doi.org/10.5281/zenodo.840129
+
+The latest DOI for the "CWL User Guide" is:
+[![DOI](https://zenodo.org/badge/89621457.svg)](https://zenodo.org/badge/latestdoi/89621457)

CITATION

@@ -1,7 +1,5 @@
----
-layout: page
-title: "Contributor Code of Conduct"
----
+# Code of Conduct
+
 As contributors and maintainers of this project,
 we pledge to respect all people who contribute through reporting issues,
 posting feature requests,
@@ -20,5 +18,3 @@ Anyone who violates this code of conduct may be sanctioned or expelled from
 these spaces at the discretion of the leadership team.
 
 For more details, see the [complete CWL project code of conduct](https://github.com/common-workflow-language/common-workflow-language/blob/master/CODE_OF_CONDUCT.md).
-
-{% include links.md %}